They have to be done well, otherwise they can ruin the appearance of a machine and make it uncomfortable to play on.
Cheap LEDs that have a low 'refresh' rate will make the ball travel look 'stuttered' when going over LED inserts. People that are most able to notice (and be offended by this) are people that use and appreciate the difference between 60hz and 144hz monitors on gaming PCs.
They also don't look exactly the same as bulbs, as LEDs are sharply on/off whereas incandescent isn't. How much this matters depends on the game. You can also mitigate this a lot with a driver board - adds expense but if you go down this line you eliminate almost all of the negatives.
Mechanical and electronic properties, however, there is no contest. LEDs are the best option, no discussion.
High quality LEDs with appropriate colours and brightness levels (including frosting, appropriate shapes of diffuser and avoiding cool white LEDs unless appropriate) and adding a good driver board - this is better in all cases except for factory-original purists, and your wallet.